adding more documentation
adding info re. mailing lists
Ignoring calculation time in AFPChainTest
Ignoring some more temp files
Removing non-ascii characters from TestSECalignment.java

Some strings contained \0 characters so that they could be compared to a
raw char[]. Removed the delimiting characters and used the proper length
variable instead.

The binary problem was discussed in comments of pull #14
Removing debugging print statement in AFPChain